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(v0.7.1.9028) predict update
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Package: AMR
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Version: 0.7.1.9027
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Version: 0.7.1.9028
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Date: 2019-08-07
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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@ -68,7 +68,7 @@ Suggests:
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VignetteBuilder: knitr
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URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
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BugReports: https://gitlab.com/msberends/AMR/issues
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License: GPL-2
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 6.1.1
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.1.9027
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# AMR 0.7.1.9028
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### Breaking
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* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
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#' @importFrom dplyr %>% pull mutate mutate_at n group_by_at summarise filter filter_at all_vars n_distinct arrange case_when n_groups transmute ungroup
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)
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#' x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010, model = "binomial")
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#' plot(x)
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#' ggplot_rsi_predict(x)
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#'
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#' x <- septic_patients %>%
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#' filter_first_isolate() %>%
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#' filter(mo_genus(mo) == "Staphylococcus") %>%
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#' resistance_predict("PEN")
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#' resistance_predict("PEN", model = "binomial")
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#' plot(x)
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#'
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#'
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#' filter(mo == as.mo("E. coli")) %>%
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#' resistance_predict(col_ab = "AMX",
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#' col_date = "date",
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#' model = "binomial",
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#' info = FALSE,
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#' minimum = 15)
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#'
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
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</span>
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</div>
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<div class="license">
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<h2>License</h2>
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<ul class="list-unstyled">
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<li><a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a></li>
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<li>
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<a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
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</li>
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</ul>
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</div>
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<div class="developers">
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
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</span>
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</div>
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@ -225,9 +225,9 @@
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</div>
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<div id="amr-0-7-1-9027" class="section level1">
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<div id="amr-0-7-1-9028" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9027" class="anchor"></a>AMR 0.7.1.9027<small> Unreleased </small>
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<a href="#amr-0-7-1-9028" class="anchor"></a>AMR 0.7.1.9028<small> Unreleased </small>
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</h1>
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<div id="breaking" class="section level3">
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<h3 class="hasAnchor">
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@ -1218,7 +1218,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-7-1-9027">0.7.1.9027</a></li>
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<li><a href="#amr-0-7-1-9028">0.7.1.9028</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
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</span>
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</div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'>resistance_predict</span>(<span class='no'>septic_patients</span>, <span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>)
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<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'>resistance_predict</span>(<span class='no'>septic_patients</span>, <span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
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<span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
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<span class='no'>x</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%>%</span>
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<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>)
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<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%>%</span>
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<span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
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<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
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<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>,
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<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>15</span>)
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@ -80,7 +80,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
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}
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\examples{
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x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)
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x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010, model = "binomial")
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plot(x)
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ggplot_rsi_predict(x)
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@ -89,7 +89,7 @@ library(dplyr)
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x <- septic_patients \%>\%
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filter_first_isolate() \%>\%
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filter(mo_genus(mo) == "Staphylococcus") \%>\%
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resistance_predict("PEN")
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resistance_predict("PEN", model = "binomial")
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plot(x)
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filter(mo == as.mo("E. coli")) \%>\%
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resistance_predict(col_ab = "AMX",
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col_date = "date",
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model = "binomial",
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info = FALSE,
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minimum = 15)
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